7QLE | pdb_00007qle

Crystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain I (aa 32-198)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7QLD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Protein stock solution of 15 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl; JCSG+ screen condition A5 (0.2 M Magnesium formate dihydrate, 20 % w/v PEG 3350) with protein end concentration of 7.5 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.127	α = 90
b = 39.036	β = 101.662
c = 60.058	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2015-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.97895	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.6	48.37	99.3	0.143	0.198	0.137	0.986	7.1	3.3		9254

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.72			0.574	0.794	0.547	0.666		3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7QLD	2.6	48.367	9252	462	99.111	0.203	0.2003	0.2	0.2583	0.26	32.184

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
2.068		-0.156	1.597		-3.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.648
r_dihedral_angle_3_deg	15.089
r_lrange_it	8.224
r_lrange_other	8.223
r_dihedral_angle_1_deg	7.237
r_mcangle_it	4.836
r_mcangle_other	4.834
r_scangle_it	4.497
r_scangle_other	4.496
r_mcbond_it	2.906
r_mcbond_other	2.902
r_scbond_it	2.708
r_scbond_other	2.706
r_angle_refined_deg	1.605
r_angle_other_deg	1.271
r_symmetry_xyhbond_nbd_refined	0.212
r_nbd_refined	0.207
r_symmetry_nbd_other	0.176
r_nbd_other	0.176
r_nbtor_refined	0.151
r_xyhbond_nbd_refined	0.144
r_symmetry_nbd_refined	0.105
r_ncsr_local_group_1	0.105
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.058
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2193
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building